Parental contribution and coefficient of coancestry among maize inbreds: Pedigree, RFLP, and SSR data

The genetic relationship between inbreds i and j can be estimated from pedigree or from molecular marker data. The objectives of this study were to: (1) determine whether pedigree, restriction fragment length polymorphism (RFLP), and simple sequence repeat (SSR) data give similar estimates of parental contribution and coefficient of coancestry (f(ij)) among a set of maize (Zea mays L.) inbreds, and (2) compare the usefulness of RFLP and SSR markers for estimating genetic relationship. We studied 13 maize inbreds with known pedigrees. The inbreds were genotyped using 124 RFLP and 195 SSR markers. For each type of marker, parental contributions were estimated from marker similarity among an inbred and both of its parents, and were subsequently used to estimate f(ij). Estimates of parental contribution differed significantly (α<0.05) between pedigree data and either type of marker, but not between the marker systems. The RFLP estimates of parental contribution failed to sum to 1.0, reflecting a higher frequency of non-parental bands with RFLP than with SSR markers. The f(ij) estimated from pedigree, RFLP, and SSR data were highly correlated (r=0.87-0.97), although significant differences were found among the three sets of f(ij) estimates. We concluded that pedigree and marker data often lead to different estimates of parental contribution and f(ij), and that SSR markers are superior to RFLP markers for estimating genetic relationship. A relevant question is whether or not the inbreds previously genotyped with an older marker system (e.g., RFLP) need to be reanalyzed with a newer marker system (e.g., SSR) for the purpose of estimating genetic relationship. Such re-analysis seems unnecessary if data for the same type of marker are available for a given inbred and both of its parents.